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[ENH] Add "chunk" entity to MRI datatype #1586

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9 changes: 6 additions & 3 deletions src/schema/objects/entities.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -51,9 +51,12 @@ chunk:
name: chunk
display_name: Chunk
description: |
The `chunk-<index>` key/value pair is used to distinguish between different regions,
2D images or 3D volumes files,
of the same physical sample with different fields of view acquired in the same imaging experiment.
The `chunk-<index>` entity is used to distinguish between different regions, 2D images (for example Microscopy),
3D volumes files, or 4D volumes files (for example DWI) of the same physical sample with different fields of
view acquired in the same imaging experiment.

In case of MRI data, this entity is used to distinguish between different anatomical regions, for example brain
and spinal cord.
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type: string
format: index
density:
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2 changes: 2 additions & 0 deletions src/schema/objects/metadata.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -404,6 +404,8 @@ ChunkTransformationMatrix:
scaling along the second and third axis respectively).
Note that non-spatial dimensions like time and channel are not included in the
transformation matrix.
In case of MRI data, the ChunkTransformationMatrix corresponds to the NIFTI [qform matrix]
(https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html)
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anyOf:
- type: array
minItems: 3
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8 changes: 8 additions & 0 deletions src/schema/rules/files/raw/anat.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ nonparametric:
reconstruction: optional
run: optional
part: optional
chunk: optional

parametric:
suffixes:
Expand Down Expand Up @@ -61,6 +62,7 @@ parametric:
ceagent: optional
reconstruction: optional
run: optional
chunk: optional

defacemask:
suffixes:
Expand All @@ -80,6 +82,7 @@ defacemask:
reconstruction: optional
run: optional
modality: optional
chunk: optional

multiecho:
suffixes:
Expand Down Expand Up @@ -122,6 +125,7 @@ multiflip:
echo: optional
flip: required
part: optional
chunk: optional

multiinversion:
suffixes:
Expand All @@ -142,6 +146,7 @@ multiinversion:
run: optional
inversion: required
part: optional
chunk: optional

mp2rage:
suffixes:
Expand All @@ -164,6 +169,7 @@ mp2rage:
flip: optional
inversion: required
part: optional
chunk: optional

vfamt:
suffixes:
Expand All @@ -187,6 +193,7 @@ vfamt:
flip: required
mtransfer: required
part: optional
chunk: optional

mtr:
suffixes:
Expand All @@ -207,3 +214,4 @@ mtr:
run: optional
mtransfer: required
part: optional
chunk: optional
2 changes: 2 additions & 0 deletions src/schema/rules/files/raw/dwi.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ dwi:
direction: optional
run: optional
part: optional
chunk: optional

sbref:
suffixes:
Expand All @@ -36,3 +37,4 @@ sbref:
direction: optional
run: optional
part: optional
chunk: optional
2 changes: 2 additions & 0 deletions src/schema/rules/files/raw/func.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ func:
run: optional
echo: optional
part: optional
chunk: optional

phase:
suffixes:
Expand All @@ -41,3 +42,4 @@ phase:
direction: optional
run: optional
echo: optional
chunk: optional